Merge branch 'bug/JAL-3718_Getdown_does_not_autoupdate_correctly' into releases/Relea...

[jalview.git] / test / jalview / ext / ensembl / EnsemblGeneTest.java

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 446b4f7..ef12ed4 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -81,7 +81,7 @@ public class EnsemblGeneTest
     // gene at (start + 10500) length 101
     SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
             null);
-    sf.setValue("ID", "gene:" + geneId);
+    sf.setValue("id", geneId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
@@ -113,7 +113,7 @@ public class EnsemblGeneTest
     // gene at (start + 10500) length 101
     SequenceFeature sf = new SequenceFeature("gene", "", 10500, 10600, 0f,
             null);
-    sf.setValue("ID", "gene:" + geneId);
+    sf.setValue("id", geneId);
     sf.setStrand("+");
     genomic.addSequenceFeature(sf);
 
@@ -146,30 +146,30 @@ public class EnsemblGeneTest
     // transcript feature
     SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
             20500, 0f, null);
-    sf1.setValue("Parent", "gene:" + geneId);
-    sf1.setValue("transcript_id", "transcript1");
+    sf1.setValue("Parent", geneId);
+    sf1.setValue("id", "transcript1");
     genomic.addSequenceFeature(sf1);
 
     // transcript sub-type feature
     SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
             0f, null);
-    sf2.setValue("Parent", "gene:" + geneId);
-    sf2.setValue("transcript_id", "transcript2");
+    sf2.setValue("Parent", geneId);
+    sf2.setValue("id", "transcript2");
     genomic.addSequenceFeature(sf2);
 
     // NMD_transcript_variant treated like transcript in Ensembl
     SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
             22000, 22500, 0f, null);
     // id matching should not be case-sensitive
-    sf3.setValue("Parent", "gene:" + geneId.toLowerCase());
-    sf3.setValue("transcript_id", "transcript3");
+    sf3.setValue("Parent", geneId.toLowerCase());
+    sf3.setValue("id", "transcript3");
     genomic.addSequenceFeature(sf3);
 
     // transcript for a different gene - ignored
     SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
             0f, null);
-    sf4.setValue("Parent", "gene:XYZ");
-    sf4.setValue("transcript_id", "transcript4");
+    sf4.setValue("Parent", "XYZ");
+    sf4.setValue("id", "transcript4");
     genomic.addSequenceFeature(sf4);
 
     EnsemblGene testee = new EnsemblGene();
@@ -196,24 +196,24 @@ public class EnsemblGeneTest
     EnsemblGene testee = new EnsemblGene();
     SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
             null);
-    sf.setValue("ID", "gene:" + geneId);
+    sf.setValue("id", geneId);
     assertFalse(testee.retainFeature(sf, geneId));
 
     sf = new SequenceFeature("transcript", "", 20000, 20500, 0f, null);
-    sf.setValue("Parent", "gene:" + geneId);
+    sf.setValue("Parent", geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
     sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
             null);
-    sf.setValue("Parent", "gene:" + geneId);
+    sf.setValue("Parent", geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
     sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
             0f, null);
-    sf.setValue("Parent", "gene:" + geneId);
+    sf.setValue("Parent", geneId);
     assertTrue(testee.retainFeature(sf, geneId));
 
-    sf.setValue("Parent", "gene:XYZ");
+    sf.setValue("Parent", "ßXYZ");
     assertFalse(testee.retainFeature(sf, geneId));
 
     sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
@@ -235,28 +235,28 @@ public class EnsemblGeneTest
     seq.addSequenceFeature(sf1);
 
     // gene with wrong ID not valid
-    SequenceFeature sf2 = new SequenceFeature("gene", "", 1, 2, 0f, null);
-    sf2.setValue("ID", "gene:XYZ");
+    SequenceFeature sf2 = new SequenceFeature("gene", "a", 1, 2, 0f, null);
+    sf2.setValue("id", "XYZ");
     seq.addSequenceFeature(sf2);
 
     // gene with right ID is valid
-    SequenceFeature sf3 = new SequenceFeature("gene", "", 1, 2, 0f, null);
-    sf3.setValue("ID", "gene:" + accId);
+    SequenceFeature sf3 = new SequenceFeature("gene", "b", 1, 2, 0f, null);
+    sf3.setValue("id", accId);
     seq.addSequenceFeature(sf3);
 
     // gene sub-type with right ID is valid
     SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
-    sf4.setValue("ID", "gene:" + accId);
+    sf4.setValue("id", accId);
     seq.addSequenceFeature(sf4);
 
     // transcript not valid:
     SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
-    sf5.setValue("ID", "gene:" + accId);
+    sf5.setValue("id", accId);
     seq.addSequenceFeature(sf5);
 
     // exon not valid:
     SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
-    sf6.setValue("ID", "gene:" + accId);
+    sf6.setValue("id", accId);
     seq.addSequenceFeature(sf6);
     
     List<SequenceFeature> sfs = new EnsemblGene()
@@ -271,18 +271,24 @@ public class EnsemblGeneTest
 
   /**
    * Check behaviour of feature colour scheme for EnsemblGene sequences.
-   * Currently coded to display exon and sequence_variant (or sub-types) only,
-   * with sequence_variant in red above exon coloured by label.
+   * Currently coded to hide all except exon and sequence_variant (or sub-types)
+   * only, with sequence_variant in red above exon coloured by label.
    */
   @Test(groups = "Functional")
   public void testGetFeatureColourScheme()
   {
     FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
-    assertTrue(fc.isFeatureDisplayed("exon"));
-    assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
-    assertTrue(fc.isFeatureDisplayed("sequence_variant"));
-    assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
-    assertFalse(fc.isFeatureDisplayed("transcript"));
+    assertFalse(fc.isFeatureDisplayed("exon"));
+    assertFalse(fc.isFeatureHidden("exon"));
+    assertFalse(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
+    assertFalse(fc.isFeatureHidden("coding_exon")); // subtype of exon
+    assertFalse(fc.isFeatureDisplayed("sequence_variant"));
+    assertFalse(fc.isFeatureHidden("sequence_variant"));
+    assertFalse(fc.isFeatureDisplayed("feature_variant")); // subtype
+    assertFalse(fc.isFeatureHidden("feature_variant")); // subtype
+    assertTrue(fc.isFeatureHidden("transcript"));
+    assertTrue(fc.isFeatureHidden("CDS"));
+
     assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
             .getColour());
     assertEquals(Color.RED, fc.getFeatureColour("feature_variant")